So I have the same problem for over half a year now and from time to time I tried reinstalling Ubunty with the hope a new gpu driver or new ubuntu version would fix this, but the problem remains:
After I log into Ubuntu, there is a random (it changes from reboot to reboot and from time to time while running Ubuntu) set of things/elements I can't click on. Examples:
The unity sidebar. I hover over the buttons/programs and clicking on them has no result, I don't even get this hover-feedback from the UI
Terminal. When I managed to get mouse-focus on the terminal, my mouse cursor changes to the text cursor and stays that way even if I try to change the focus to another window (firefox for example)
System settings. I can't click on options, buttons or anything
Firefox, sometimes I randomly manage to get focus to an opened firefox window, but I can't click on the resize/exit button, I can't move the window. Again, as in the previous examples, no visual UI-feedback when I hover on certain elements
Sometimes certain applications work for a while in the sense that I can click on everything with normal response (the Unity sidebar is also working from time to time). Here some things I can remember I tried:
Ubuntu 15: started using Unity, didn't work. Removed Unity and installed Gnome, didn't work. Tried nouveau and most recent GPU driver (nvidia), didn't work.
Ubuntu 16: Tried the Gnome-version couple of weeks ago when 16 was beta, didn't work. Tried it today with the normal Unity-version of the release-version of Ubuntu 16, immediately didn't work properly after the first reboot with nouveau drivers for GPU. I activated the nvidia prop. drivers in the 'Software & Updates' settings (version 361 iirc), doesn't work either.
On both OS versions, I did some compiz stuff I didn't completely understand (basically telling compiz to reconfigure and unity to restart), but that also didn't work
I'm not a linux guru, no idea what else I could try. This is my hardware: Intel i7, Nvidia GTX 980 TI, Asus Z97 Killer Motherboard, Zowie Gaming Mouse (USB) 7. Any ideas?